---
title: "DNA Extraction"
author: "Pierre Barry"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
output: 
  flexdashboard::flex_dashboard:
    theme: paper
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: scroll
---

```{r global, include=FALSE}
list.of.packages <- c("RColorBrewer","readxl","DT","ggplot2","plotly","png")

for (i in list.of.packages){
  if (i %in% installed.packages()[,"Package"] == FALSE){
    install.packages(i)
  }
  eval(bquote(library(.(i))))
}
```

```{r, include = FALSE}
color_med_atl=data.frame(Location=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                         Col=brewer.pal(n = 4, name = "RdBu"))
```

DNA extraction {data-icon="ion-beaker"}
=======================================================================

```{r}
extraction <- as.data.frame(read_excel(paste(path,"/data/dna_extraction/dna_extraction.xlsx",sep=""),sheet="REORDER"))

LOCATION=c()
for (i in 1:nrow(extraction)){
  if (nchar(extraction$SAMPLE_ID[i])==8){
    LOCATION[i]=substr(extraction$SAMPLE_ID[i],start=6,stop=7)
  } else {
    LOCATION[i]=substr(extraction$SAMPLE_ID[i],start=6,stop=7)
  }
}
LOCATION=factor(LOCATION,levels=c("Li","Mu","Fa","Ga"),
                labels=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"))
extraction$LOCATION=LOCATION

extraction$SPECIES_CODE=factor(extraction$SPECIES_CODE)
labels_species=c()
for (sp in 1:length(levels(extraction$SPECIES_CODE))){
  
  labels_species=c(labels_species,
                   paste(levels(extraction$SPECIES_CODE)[sp]," \n n = ",table(extraction$SPECIES_CODE)[sp],sep=" "))
  
}
labels_species=as.vector(labels_species)
extraction$Conc=as.numeric(extraction$Conc)
extraction$Sequenced=factor(extraction$Sequenced)
extraction$Flowcell=factor(extraction$Flowcell)
extraction$Conc_Qubit=as.numeric(extraction$Conc_Qubit)
```

Row {.tabset}
-----------------

### Table {data-height=750}

```{r}
datatable(extraction, 
          class = 'cell-border stripe',
          rownames = FALSE,
          filter = 'top', options = list(
          pageLength = 100,autowidth=T,scrollY=500,scrollX=100))
```

### Nanodrop concentration

```{r}
ppp <- ggplot(extraction, aes(x=SPECIES_CODE, y=Conc))  +
  geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
  #geom_boxplot(outlier.shape = NA,
  #             outlier.size = 0.000001,
  #             alpha=0.5,
  #             width=0.1,
  #             show.legend = F)+
  geom_point(aes(col=LOCATION,
                 size=Sequenced,
                 shape=Flowcell,
                 text=paste("Sample: ",SAMPLE_ID, " \n Conc.:",Conc,sep="")),
             position='jitter',
             alpha=0.75)+
  #stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
  stat_summary(fun=median, geom="point", size=2, color="orange")+
  scale_x_discrete(name="Species",
                   labels=labels_species)+
  ylab("Nanodrop concentration (ng/ul)")+
  xlab("Species")+
  theme_classic()+
  scale_colour_manual(name = "",
                      labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                      values = brewer.pal(n = 4, name = "RdBu"))+
  scale_size_manual(name = "",
                      labels = c("0","1"),
                      values = c(1,1.5))+
  theme(legend.position="bottom")
ppp<-ggplotly(ppp,height=500,tooltip=c("text"))  %>% partial_bundle() 
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[1], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img2)),
        x = vv[2], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[3], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[4], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[5], y = 1, 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[6], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[7], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[8], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[9], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[10], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[11], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[12], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[13], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[14],y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[15], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[16], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[17], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[18], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[20], y = 1, 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 

ppp
```

### Qubit concentration

```{r}
ppp <- ggplot(extraction, aes(x=SPECIES_CODE, y=Conc_Qubit))  +
  geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
  #geom_boxplot(outlier.shape = NA,
  #             outlier.size = 0.000001,
  #             alpha=0.5,
  #             width=0.1,
  #             show.legend = F)+
  geom_point(aes(col=LOCATION,
                 size=Sequenced,
                 shape=Flowcell,
                 text=paste("Sample: ",SAMPLE_ID, " \n Qubit Conc.:",Conc_Qubit,sep="")),
             position='jitter',
             alpha=0.75)+
  #stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
  stat_summary(fun=median, geom="point", size=2, color="orange")+
  scale_x_discrete(name="Species",
                   labels=labels_species)+
  ylab("Qubit concentration (ng/ul)")+
  xlab("Species")+
  theme_classic()+
  scale_colour_manual(name = "",
                      labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                      values = brewer.pal(n = 4, name = "RdBu"))+
  scale_size_manual(name = "",
                      labels = c("0","1"),
                      values = c(1,1.5))+
  theme(legend.position="bottom")
ppp<-ggplotly(ppp,height=500,tooltip=c("text"))  %>% partial_bundle() 
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[1], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img2)),
        x = vv[2], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[3], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[4], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[5], y = 1, 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[6], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[7], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[8], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[9], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[10], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[11], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[12], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[13], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[14],y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[15], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[16], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[17], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[18], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[20], y = 1, 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 

ppp
```


### A260/A280

```{r}
ppp <- ggplot(extraction, aes(x=SPECIES_CODE, y=A260/A280))  +
  geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
  #geom_boxplot(outlier.shape = NA,
  #             outlier.size = 0.000001,
  #             alpha=0.5,
  #             width=0.1,
  #             show.legend = F)+
  geom_point(aes(col=LOCATION,
                 size=Sequenced,
                 shape=Flowcell,
                 text=paste("Sample: ",SAMPLE_ID, " \n A260/280:",A260/A280,sep="")),
             position='jitter',
             alpha=0.75)+
  geom_hline(yintercept = 1.8,col="red",linetype="dashed",alpha=0.5)+
  geom_hline(yintercept = 2.0,col="red",linetype="dashed",alpha=0.5)+  
  #stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
  stat_summary(fun=median, geom="point", size=2, color="orange")+
  scale_x_discrete(name="Species",
                   labels=labels_species)+
  ylab("A260/A280")+
  xlab("Species")+
  theme_classic()+
  scale_colour_manual(name = "",
                      labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                      values = brewer.pal(n = 4, name = "RdBu"))+
  scale_size_manual(name = "",
                      labels = c("0","1"),
                      values = c(1,1.5))+
  theme(legend.position="bottom")
ppp<-ggplotly(ppp,height=500,tooltip=c("text"))  %>% partial_bundle() 
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[1], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img2)),
        x = vv[2], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[3], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[4], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[5], y = 1, 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[6], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[7], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[8], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[9], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[10], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[11], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[12], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[13], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[14],y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[15], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[16], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[17], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[18], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[20], y = 1, 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 

ppp
```

### A260/A230

```{r}
ppp <- ggplot(extraction, aes(x=SPECIES_CODE, y=A260230))  +
  geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
  #geom_boxplot(outlier.shape = NA,
  #             outlier.size = 0.000001,
  #             alpha=0.5,
  #             width=0.1,
  #             show.legend = F)+
  geom_point(aes(col=LOCATION,
                 size=Sequenced,
                 shape=Flowcell,
                 text=paste("Sample: ",SAMPLE_ID, " \n A260/230:",A260230,sep="")),
             position='jitter',
             alpha=0.75)+
  geom_hline(yintercept = 2.0,col="red",linetype="dashed",alpha=0.5)+
  geom_hline(yintercept = 2.2,col="red",linetype="dashed",alpha=0.5)+  
  #stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
  stat_summary(fun=median, geom="point", size=2, color="orange")+
  scale_x_discrete(name="Species",
                   labels=labels_species)+
  ylab("A260/A230")+
  xlab("Species")+
  theme_classic()+
  scale_colour_manual(name = "",
                      labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                      values = brewer.pal(n = 4, name = "RdBu"))+
  scale_size_manual(name = "",
                      labels = c("0","1"),
                      values = c(1,1.5))+
  theme(legend.position="bottom")
ppp<-ggplotly(ppp,height=500,tooltip=c("text"))  %>% partial_bundle() 
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[1], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img2)),
        x = vv[2], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[3], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[4], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[5], y = 1, 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[6], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[7], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[8], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[9], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[10], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[11], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[12], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[13], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[14],y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[15], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[16], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[17], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[18], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = 1, 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[20], y = 1, 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 

ppp
```

Packages used {data-icon="fa-map"}
=======================================================================

```{r}
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
```